Fix/sentieon gvcftyper intervals

modules/nf-core/sentieon/gvcftyper/main.nf

@@ -10,10 +10,10 @@ process SENTIEON_GVCFTYPER {
 
     input:
     tuple val(meta), path(gvcfs), path(tbis), path(intervals)
-    tuple val(meta1), path(fasta)
-    tuple val(meta2), path(fai)
-    tuple val(meta3), path(dbsnp)
-    tuple val(meta4), path(dbsnp_tbi)
+    tuple val(meta2), path(fasta)
+    tuple val(meta3), path(fai)
+    tuple val(meta4), path(dbsnp)
+    tuple val(meta5), path(dbsnp_tbi)
 
     output:
     tuple val(meta), path("*.vcf.gz"),     emit: vcf_gz
@@ -27,13 +27,20 @@ process SENTIEON_GVCFTYPER {
     def prefix = task.ext.prefix ?: "${meta.id}_genotyped"
     def gvcfs_input = '-v ' + gvcfs.join(' -v ')
     def dbsnp_cmd = dbsnp ? "--dbsnp ${dbsnp}" : ""
+    def interval_command = intervals ? "--interval ${intervals}" : ""
     def sentieonLicense = secrets.SENTIEON_LICENSE_BASE64
         ? "export SENTIEON_LICENSE=\$(mktemp);echo -e \"${secrets.SENTIEON_LICENSE_BASE64}\" | base64 -d > \$SENTIEON_LICENSE; "
         : ""
     """
     ${sentieonLicense}
 
-    sentieon driver -r ${fasta} --algo GVCFtyper ${gvcfs_input} ${dbsnp_cmd} ${prefix}.vcf.gz
+    sentieon driver \\
+        -r ${fasta} \\
+        ${interval_command} \\
+        --algo GVCFtyper \\
+        ${gvcfs_input} \\
+        ${dbsnp_cmd} \\
+        ${prefix}.vcf.gz
 
     """
 

modules/nf-core/sentieon/gvcftyper/meta.yml

@@ -33,10 +33,10 @@ input:
         ontologies: []
     - intervals:
         type: file
-        description: Interval file with the genomic regions included in the library
-          (optional)
+        description: Interval file with the genomic regions included in the
+          library (optional)
         ontologies: []
-  - - meta1:
+  - - meta2:
         type: map
         description: |
           Groovy Map containing sample information
@@ -46,7 +46,7 @@ input:
         description: Reference fasta file
         pattern: "*.fasta"
         ontologies: []
-  - - meta2:
+  - - meta3:
         type: map
         description: |
           Groovy Map containing sample information
@@ -56,7 +56,7 @@ input:
         description: Reference fasta index file
         pattern: "*.fai"
         ontologies: []
-  - - meta3:
+  - - meta4:
         type: map
         description: |
           Groovy Map containing sample information
@@ -66,8 +66,8 @@ input:
         description: dbSNP VCF file
         pattern: "*.vcf.gz"
         ontologies:
-          - edam: http://edamontology.org/format_3989 # GZIP format
-  - - meta4:
+          - edam: http://edamontology.org/format_3989
+  - - meta5:
         type: map
         description: |
           Groovy Map containing sample information
@@ -89,7 +89,7 @@ output:
           description: VCF file
           pattern: "*.vcf.gz"
           ontologies:
-            - edam: http://edamontology.org/format_3989 # GZIP format
+            - edam: http://edamontology.org/format_3989
   vcf_gz_tbi:
     - - meta:
           type: map
@@ -109,7 +109,7 @@ output:
           type: string
           description: The tool name
       - sentieon driver --version | sed "s/.*-//g":
-          type: string
+          type: eval
           description: The command used to generate the version of the tool
 topics:
   versions:
@@ -120,7 +120,7 @@ topics:
           type: string
           description: The tool name
       - sentieon driver --version | sed "s/.*-//g":
-          type: string
+          type: eval
           description: The command used to generate the version of the tool
 authors:
   - "@asp8200"